Merge branch 'drieslab:suite' into suite

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.0.6
+Version: 4.0.8
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
-		 role = c("aut", "cre")),
+		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
 	person("Jiaji", "George Chen", email = "[email protected]",
 		 role = c("aut")),
 	person("Joselyn C.", "Chávez-Fuentes", email = "[email protected]",
@@ -19,20 +19,19 @@ Authors@R: c(
 	person("Natalie", "Del Rossi", email = "[email protected]",
 		 role = c("aut"))
 	)
-Maintainer: Ruben Dries <[email protected]>
 Description: Toolbox to process, analyze and visualize spatial single-cell expression data.
-License: GPL (>= 3)
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
 BugReports: https://github.com/drieslab/Giotto/issues
 RoxygenNote: 7.3.1
 Depends:
-    base (>= 3.5.0),
-    utils (>= 3.5.0),
-    R (>= 3.5.0),
+    base (>= 4.1.0),
+    utils (>= 4.1.0),
+    R (>= 4.1.0),
     methods,
-    GiottoClass (>= 0.3.0)
+    GiottoClass (>= 0.3.1)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -42,12 +41,12 @@ Imports:
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
     ggrepel,
-    GiottoUtils (>= 0.1.6),
-    GiottoVisuals (>= 0.2.0),
+    GiottoUtils (>= 0.1.8),
+    GiottoVisuals (>= 0.2.2),
     igraph (>= 1.2.4.1),
     jsonlite,
     limma,
-    Matrix (>= 1.6.2),
+    Matrix (>= 1.6-2),
     MatrixGenerics,
     plotly,
     progressr,
@@ -164,6 +163,6 @@ Collate:
     'variable_genes.R'
     'wnn.R'
     'zzz.R'
-biocViews:
+biocViews: Software, Technology, Spatial, SingleCell, Transcriptomics
 VignetteBuilder: knitr
 Config/testthat/edition: 3

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: Giotto authors

NAMESPACE

@@ -145,8 +145,8 @@ export(create_jackstrawplot)
 export(create_screeplot)
 export(crop)
 export(cropGiottoLargeImage)
-export(crossSectionGenePlot)
-export(crossSectionGenePlot3D)
+export(crossSectionFeatPlot)
+export(crossSectionFeatPlot3D)
 export(crossSectionPlot)
 export(crossSectionPlot3D)
 export(detectSpatialCorFeats)
@@ -258,7 +258,7 @@ export(heatmSpatialCorGenes)
 export(hexVertices)
 export(hyperGeometricEnrich)
 export(initHMRF_V2)
-export(insertCrossSectionGenePlot3D)
+export(insertCrossSectionFeatPlot3D)
 export(insertCrossSectionSpatPlot3D)
 export(installGiottoEnvironment)
 export(instructions)

NEWS.md

@@ -1,10 +1,26 @@
 
+# Giotto 4.0.8 (2024/05/22)
+
+## Breaking changes
+* `crossSectionGenePlot()` removed. Use `crossSectionFeatPlot()` instead
+* `crossSectionGenePlot3D()` removed. Use `crossSectionFeatPlot3D()` instead
+* `insertCrossSectionGenePlot3D()` removed Use `insertCrossSectionFeatPlot3D()` instead
+
+## Bug fixes
+* `binSpect()` param passing error introduced in _v4.0.6_
+* updated `viewHMRFresults3D()` and `viewHMRFresults2D()`
+* updated `createCrossSections()`, `insertCrossSectionSpatPlot3D()`, `crossSectionPlot()`, `crossSectionFeatPlot3D()`, `insertCrossSectionFeatPlot3D()`, `crossSectionPlot3D()`, `crossSectionFeatPlot()`
+
+## Changes
+* GiottoVisuals (>= 0.2.2), GiottoClass (>= 0.3.1), GiottoUtils (>= 0.1.8) are now required.
+
 # Giotto 4.0.6 (2024/05/13)
 
 ## Enhancements
 * New `interpolateFeature()` for kriging interpolation of values
 
-
+## Changes
+* GiottoVisuals (>= 0.2.0) and GiottoClass (>= 0.3.0) are now required.